Job ID = 10937638 sra ファイルのダウンロード中... Completed: 140924K bytes transferred in 5 seconds (213151K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 4401803 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3463289/SRR6367828.sra Written 4401803 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3463289/SRR6367828.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:46 4401803 reads; of these: 4401803 (100.00%) were unpaired; of these: 674305 (15.32%) aligned 0 times 3270609 (74.30%) aligned exactly 1 time 456889 (10.38%) aligned >1 times 84.68% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2177624 / 3727498 = 0.5842 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 10 Aug 2018 02:44:31: # Command line: callpeak -t SRX3463289.bam -f BAM -g 12100000 -n SRX3463289.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3463289.10 # format = BAM # ChIP-seq file = ['SRX3463289.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Aug 2018 02:44:31: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:44:31: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:44:31: # Command line: callpeak -t SRX3463289.bam -f BAM -g 12100000 -n SRX3463289.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3463289.05 # format = BAM # ChIP-seq file = ['SRX3463289.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Aug 2018 02:44:31: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:44:31: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:44:31: # Command line: callpeak -t SRX3463289.bam -f BAM -g 12100000 -n SRX3463289.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3463289.20 # format = BAM # ChIP-seq file = ['SRX3463289.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Aug 2018 02:44:31: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:44:31: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:44:38: 1000000 INFO @ Fri, 10 Aug 2018 02:44:38: 1000000 INFO @ Fri, 10 Aug 2018 02:44:39: 1000000 INFO @ Fri, 10 Aug 2018 02:44:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Aug 2018 02:44:42: #1 tag size = 50 INFO @ Fri, 10 Aug 2018 02:44:42: #1 total tags in treatment: 1549874 INFO @ Fri, 10 Aug 2018 02:44:42: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:44:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:44:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Aug 2018 02:44:42: #1 tag size = 50 INFO @ Fri, 10 Aug 2018 02:44:42: #1 total tags in treatment: 1549874 INFO @ Fri, 10 Aug 2018 02:44:42: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:44:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:44:42: #1 tags after filtering in treatment: 1549874 INFO @ Fri, 10 Aug 2018 02:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:44:42: #1 finished! INFO @ Fri, 10 Aug 2018 02:44:42: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:44:42: #1 tags after filtering in treatment: 1549874 INFO @ Fri, 10 Aug 2018 02:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:44:42: #1 finished! INFO @ Fri, 10 Aug 2018 02:44:42: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:44:42: #2 number of paired peaks: 145 WARNING @ Fri, 10 Aug 2018 02:44:42: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Aug 2018 02:44:42: start model_add_line... INFO @ Fri, 10 Aug 2018 02:44:42: #2 number of paired peaks: 145 WARNING @ Fri, 10 Aug 2018 02:44:42: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Aug 2018 02:44:42: start model_add_line... INFO @ Fri, 10 Aug 2018 02:44:42: start X-correlation... INFO @ Fri, 10 Aug 2018 02:44:42: end of X-cor INFO @ Fri, 10 Aug 2018 02:44:42: #2 finished! INFO @ Fri, 10 Aug 2018 02:44:42: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Aug 2018 02:44:42: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Aug 2018 02:44:42: #2.2 Generate R script for model : SRX3463289.05_model.r INFO @ Fri, 10 Aug 2018 02:44:42: start X-correlation... INFO @ Fri, 10 Aug 2018 02:44:42: end of X-cor INFO @ Fri, 10 Aug 2018 02:44:42: #2 finished! INFO @ Fri, 10 Aug 2018 02:44:42: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Aug 2018 02:44:42: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Aug 2018 02:44:42: #2.2 Generate R script for model : SRX3463289.10_model.r INFO @ Fri, 10 Aug 2018 02:44:42: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:44:42: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:44:44: #1 tag size is determined as 50 bps INFO @ Fri, 10 Aug 2018 02:44:44: #1 tag size = 50 INFO @ Fri, 10 Aug 2018 02:44:44: #1 total tags in treatment: 1549874 INFO @ Fri, 10 Aug 2018 02:44:44: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:44:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:44:44: #1 tags after filtering in treatment: 1549874 INFO @ Fri, 10 Aug 2018 02:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:44:44: #1 finished! INFO @ Fri, 10 Aug 2018 02:44:44: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:44:44: #2 number of paired peaks: 145 WARNING @ Fri, 10 Aug 2018 02:44:44: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Aug 2018 02:44:44: start model_add_line... INFO @ Fri, 10 Aug 2018 02:44:44: start X-correlation... INFO @ Fri, 10 Aug 2018 02:44:44: end of X-cor INFO @ Fri, 10 Aug 2018 02:44:44: #2 finished! INFO @ Fri, 10 Aug 2018 02:44:44: #2 predicted fragment length is 166 bps INFO @ Fri, 10 Aug 2018 02:44:44: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 10 Aug 2018 02:44:44: #2.2 Generate R script for model : SRX3463289.20_model.r INFO @ Fri, 10 Aug 2018 02:44:44: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:44:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:44:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:44:48: #4 Write output xls file... SRX3463289.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:44:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:44:48: #4 Write peak in narrowPeak format file... SRX3463289.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:44:48: #4 Write summits bed file... SRX3463289.05_summits.bed INFO @ Fri, 10 Aug 2018 02:44:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (822 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:44:49: #4 Write output xls file... SRX3463289.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:44:49: #4 Write peak in narrowPeak format file... SRX3463289.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:44:49: #4 Write summits bed file... SRX3463289.10_summits.bed INFO @ Fri, 10 Aug 2018 02:44:49: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (463 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:44:50: #4 Write output xls file... SRX3463289.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:44:51: #4 Write peak in narrowPeak format file... SRX3463289.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:44:51: #4 Write summits bed file... SRX3463289.20_summits.bed INFO @ Fri, 10 Aug 2018 02:44:51: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (233 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。